I want to build a new system, using ECC-RAM. That has not do with handbrake. It can be AMD or Intel. It looks like with AMD the options are very limited regarding a board with ECC (Asus only?). So I am looking to Intel and I think Xeon-cpus could be an option, which are more expensive of course. For the moment I want to pay about 400-500€ for the board and the cpu.

Does anyone have a link to benchmarks re handbrake an Xeon, so I can see if I get the same percentage of more speed compared to the price of an AMD system?

Should be a solid performer. Generally speaking, the recommended processor for HandBrake (or any software that uses x264 for video encoding) would be a 4-to-6 core Intel processor clocked as high as you can afford.

Depending on your encoding habits (archival vs. throwaway encodes for use on e.g. mobile devices), getting a processor with Quick Sync Video hardware may be worthwhile (compression efficiency can't rival x264 when using slow settings, but QSV is quite fast and energy-efficient, so it's a pretty good alternative when compression efficiency isn't the primary goal). We don't yet support QSV under Linux (Windows-only for now), though this should hopefully change soon.

As a minor question, does it make sense for the future, if a Nvidia GT610 or GT720 graphics adapter is used, or should I even think to spend more money for the graphics card. I use kdenlive for video cutting.

Just a reminder... whatever you put together, make sure you get the cooling right. You don't want the BIOS cutting back on your speed because the CPU hits its temp limits during long encodes.

(I forgot to turn on my auxiliary cooling fan on one of my computers during the current encode... even with a massive heat sink, moving the hot air out of the case makes a 6C difference. need to put a thermal sensor on the stupid thing....)

ECC RAM is nice -- some even say essential -- but there is very little real-world data. I am looking for empirical data myself.

Even on PCs that support ECC RAM, the OS typically does not show the number of soft errors, which is what we are interested in.

Well, googling seems to indicate that on Linux, the errors are logged to mcelog. (At least this is true for RHEL 6.x.)

Results:
11 out of 81 PCs have non-zero mcelog. Out of the 11, 4 have memory scrubbing errors, which I think means an ECC soft error. 3 of them are bad RAM -- the errors are logged within a short span of time. Which means only one is real, and it occurs only once. These PCs have 12 - 64 GB RAM and have been running mostly 24/7 for 1-2+ years.